GenPipes 4.6.0 Release Notes

What’s new?

This is a medium release with bug-fixes:

  • General for all pipelines:
    • Fixed an issue with using zless by replacing it with zcat. This issue recently appeared on alliance clusters and may have been related to the upgrades to the StdEnv module. We encourage all users working on alliance clusters to use the new version of GenPipes!

  • Amplicon Sequencing Pipeline :
    • Bug fixes and improved module loading in qiime protocol

  • Methyl Sequencing Pipeline :
    • Reverted BisSNP to v.0.82.2 because v.1.0.0 was outputting malformed vcf files

    • Added gzipping of BisSNP output files

  • Tumor Pair Pipeline :
    • Fixed a bug with PCGR when pair name is longer than 35 characters

    • Improved restarts

  • RNA Sequencing Pipeline :
    • Fixed a bug with PCGR when sample name is longer than 35 characters

    • Minor changes to resource requests for improving efficiency

  • Chip Sequencing Pipeline :
    • Fixed an error that caused the same blacklist file to be used regardless of species and genome version specified. Use of a blacklist is now optional and users can now specify their desired blacklist file in their config file.

  • Cov Sequencing Pipeline :
    • The default version of amplicon scheme is now updated to v.5.3.2

    • The pandoc version for report generation to 2.16.2

Quick! Where can I find it? I can’t wait!

Where is the detailed ChangeLog?

A ChangeLog ( is available in the archive as well as in the repository.

Since we use git, there are many ways to get the details in many formats.

One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert, which lists the commits by tag and author.

Enjoy our pipelines installed on the many Compute Canada clusters! We look forward to your feedback!